Contacts of the strand formed by residues 96 - 103 (chain A) in PDB entry 3L4U
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A GLN* 2.9 38.2 + - - +
93A THR* 3.0 58.4 + - + +
94A SER 3.7 0.2 - - - -
95A ASN* 1.3 81.6 - - - +
97A PHE* 1.3 65.5 + - - +
119A PHE* 5.5 2.8 - - - -
129A TYR* 3.0 15.5 + - - -
263A TYR* 4.1 7.0 - - + -
264A VAL 3.4 4.0 - - - +
265A PHE* 3.6 35.0 - - + -
276A GLU* 4.7 8.1 + - - +
279A GLU* 3.9 26.9 + - - +
280A LEU* 3.9 23.9 - - - +
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Residues in contact with PHE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA* 3.6 29.4 - - + -
90A GLU 3.4 18.8 - - - -
91A TYR* 4.3 8.3 - + - -
96A ARG* 1.3 74.3 - - - +
98A HIS* 1.3 70.0 + - - +
99A PHE* 3.5 31.4 - + + -
129A TYR* 3.6 33.6 - + + -
131A VAL* 3.6 28.9 - - + -
140A ILE* 3.9 10.3 - - + -
142A VAL* 3.7 21.3 - - + -
263A TYR* 3.3 5.9 - - - +
264A VAL* 2.8 42.9 + - + +
266A LEU* 6.1 0.4 - - + -
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Residues in contact with HIS 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A THR 4.0 0.8 - - - +
89A ALA* 3.4 0.7 - - - -
90A GLU* 2.8 69.1 + - + +
92A GLN* 3.2 28.2 - - + +
97A PHE* 1.3 77.1 - - - +
99A PHE* 1.3 63.1 + - - +
100A LYS* 4.0 23.9 + - + +
261A ASP* 2.4 36.9 + - - -
262A PHE 3.2 12.8 + - - -
263A TYR* 3.3 27.7 + + + -
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Residues in contact with PHE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 4.0 21.5 - - + -
88A THR 3.2 11.0 - - - +
89A ALA* 4.3 1.6 - - - -
97A PHE* 3.5 31.2 - + + -
98A HIS* 1.3 77.0 - - - +
100A LYS* 1.3 63.7 + - - +
101A LEU* 4.4 11.7 - - + -
140A ILE* 4.0 19.1 - - + -
142A VAL* 5.3 0.9 - - + -
152A PHE* 3.6 36.1 - + - -
168A LEU* 4.0 11.7 - - + -
260A LEU 4.0 0.4 - - - +
261A ASP* 4.0 0.3 - - - +
262A PHE* 2.8 70.8 + + + +
264A VAL* 4.4 13.0 - - + -
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU 3.4 2.6 - - - +
87A LEU* 3.4 3.7 - - - +
88A THR* 2.9 46.9 + - + +
98A HIS* 4.0 19.0 + - + +
99A PHE* 1.3 76.6 - - - +
101A LEU* 1.3 62.0 + - - +
102A THR* 4.0 15.7 - - + -
110A GLU* 2.8 37.3 + - - -
259A ILE* 4.1 7.2 - - + -
260A LEU 3.4 3.8 - - - -
261A ASP* 3.8 24.4 + - + +
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU* 3.7 30.5 - - + -
85A VAL* 3.8 13.7 - - + -
86A LEU 3.3 4.5 - - - -
87A LEU* 3.7 26.7 - - + -
99A PHE* 4.4 10.3 - - + -
100A LYS* 1.3 75.1 - - - +
102A THR* 1.3 60.1 + - - +
138A PHE* 4.4 9.4 - - + -
159A LEU* 3.9 26.2 - - + -
161A PHE* 3.3 21.2 - - + -
168A LEU* 4.4 15.0 - - + -
259A ILE* 3.5 17.0 - - - +
260A LEU* 3.0 27.6 + - + +
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Residues in contact with THR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A VAL* 3.3 8.0 - - - +
86A LEU* 2.8 52.8 + - - +
88A THR* 5.0 1.7 + - - -
100A LYS* 4.0 16.6 + - + -
101A LEU* 1.3 79.0 - - - +
103A ASP* 1.3 64.5 + - - +
104A GLN* 5.3 0.2 - - - -
106A ASN 5.7 0.4 - - - -
110A GLU* 4.0 11.9 - - - +
161A PHE* 4.0 8.7 - - - -
259A ILE* 3.8 29.8 - - + -
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Residues in contact with ASP 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A VAL* 3.6 31.8 - - + +
84A ASN 3.6 9.2 + - - +
102A THR* 1.3 77.4 + - - +
104A GLN* 1.3 65.0 + - - +
105A THR* 2.8 22.6 + - - +
106A ASN* 3.1 51.2 + - - +
108A ARG* 3.8 22.0 + - - +
161A PHE* 4.0 4.6 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il